public class AaSubstitutionMatrix extends Object implements Serializable
Modifier and Type | Field and Description |
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static AaSubstitutionMatrix |
allSubstitutions
Substitution matrix allowing all substitutions.
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static AaSubstitutionMatrix[] |
defaultMutationMatrices
Returns the implemented default substitution matrices.
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static AaSubstitutionMatrix |
noSubstitution
Empty substitution matrix.
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static AaSubstitutionMatrix |
singleBaseSubstitution
Substitution matrix allowing for a single base substitution.
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static AaSubstitutionMatrix |
synonymousVariant
Substitution matrix grouping synonymous amino acids.
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static AaSubstitutionMatrix |
transitionsSingleBaseSubstitution
Substitution matrix allowing for a single base transition variant.
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static AaSubstitutionMatrix |
transversalSingleBaseSubstitution
Substitution matrix allowing for a single base transversion variant.
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Constructor and Description |
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AaSubstitutionMatrix(String name,
String description)
Constructor.
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Modifier and Type | Method and Description |
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void |
add(AaSubstitutionMatrix otherMatrix)
Adds the content of a substitution matrix in this matrix.
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void |
addSubstitution(Character originalAa,
Character substitutionAa)
Adds a possible substitution.
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String |
getDescription()
Returns the description of this substitution matrix.
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String |
getName()
Returns the name of this substitution matrix.
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HashSet<Character> |
getOriginalAminoAcids()
Returns the amino acids where a substitution has been registered.
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HashSet<Character> |
getOriginalAminoAcids(Character substitutedAminoAcid)
Returns the possible original amino acids for the given substituted amino
acid as a list of their single letter code.
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HashSet<Character> |
getSubstitutionAminoAcids()
Returns the possible substituted amino acids.
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HashSet<Character> |
getSubstitutionAminoAcids(Character originalAminoAcid)
Returns the possible substituted amino acids for the given amino acid as
a list of their single letter code.
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boolean |
isSameAs(AaSubstitutionMatrix aaSubstitutionMatrix)
Indicates whether the given AaSubstitutionMatrix is the same as this one.
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void |
setDescription(String description)
Sets the description of this substitution matrix.
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void |
setName(String name)
Sets the name of this substitution matrix.
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String |
toString() |
public static final AaSubstitutionMatrix noSubstitution
public static final AaSubstitutionMatrix singleBaseSubstitution
public static final AaSubstitutionMatrix transitionsSingleBaseSubstitution
public static final AaSubstitutionMatrix transversalSingleBaseSubstitution
public static final AaSubstitutionMatrix allSubstitutions
public static final AaSubstitutionMatrix synonymousVariant
public static final AaSubstitutionMatrix[] defaultMutationMatrices
public void addSubstitution(Character originalAa, Character substitutionAa)
originalAa
- the original amino acid represented by its single
letter codesubstitutionAa
- the substituted amino acid represented by its
single letter codepublic HashSet<Character> getSubstitutionAminoAcids(Character originalAminoAcid)
originalAminoAcid
- the amino acid of interestpublic HashSet<Character> getOriginalAminoAcids(Character substitutedAminoAcid)
substitutedAminoAcid
- the substitution amino acid of interestpublic HashSet<Character> getOriginalAminoAcids()
public HashSet<Character> getSubstitutionAminoAcids()
public void add(AaSubstitutionMatrix otherMatrix)
otherMatrix
- the other matrix to addpublic String getName()
public void setName(String name)
name
- the name of this substitution matrixpublic String getDescription()
public void setDescription(String description)
description
- the description of this substitution matrixpublic boolean isSameAs(AaSubstitutionMatrix aaSubstitutionMatrix)
aaSubstitutionMatrix
- the substitution matrixCopyright © 2018. All rights reserved.